\name{confint.merMod}
\alias{confint.merMod}
\alias{confint.thpr}
\title{Compute Confidence Intervals for Parameters of a [ng]lmer Fit}
\description{
  Compute confidence intervals on the parameters of a \code{*lmer()}
  model fit (of class\code{"\linkS4class{merMod}"}).
}
\usage{
\method{confint}{merMod}(object, parm, level = 0.95,
	method = c("profile", "Wald", "boot"), zeta,
	nsim = 500,
        boot.type = c("perc","basic","norm"),
        FUN = NULL, quiet = FALSE,
	oldNames = TRUE, ...)
\method{confint}{thpr}(object, parm, level = 0.95,
        zeta, non.mono.tol=1e-2,
	...)
}

\arguments{
  \item{object}{a fitted [ng]lmer model or profile}
  \item{parm}{parameters for which intervals are sought. Specified by an
    integer vector of positions, \code{\link{character}} vector of
    parameter names, or (unless doing parametric bootstrapping with a
    user-specified bootstrap function) \code{"theta_"} or \code{"beta_"}
    to specify variance-covariance or fixed effects parameters only: see the
    \code{which} parameter of \code{\link[=profile.merMod]{profile}}.}
  \item{level}{confidence level \eqn{< 1}, typically above 0.90.}
  \item{method}{a \code{\link{character}} string determining the method
    for computing the confidence intervals.}
  \item{zeta}{(for \code{method = "profile"} only:) likelihood cutoff
    (if not specified, as by default, computed from \code{level}).}
  \item{nsim}{number of simulations for parametric bootstrap intervals.}
  \item{FUN}{bootstrap function; if \code{NULL}, an internal function
    that returns the fixed-effect parameters as well as the
    random-effect parameters on the standard deviation/correlation scale
    will be used. See \code{\link{bootMer}} for details.}
  \item{boot.type}{bootstrap confidence interval type, as described
    in \code{\link[boot]{boot.ci}}. (Methods \sQuote{stud} and \sQuote{bca}
    are unavailable because they require additional components to be
    calculated.)}
  \item{quiet}{(logical) suppress messages about computationally intensive profiling?}
  \item{oldNames}{(logical) use old-style names for variance-covariance
    parameters, e.g. \code{".sig01"}, rather than newer (more informative) names such as
    \code{"sd_(Intercept)|Subject"}? (See \code{signames} argument to
    \code{\link{profile}}).}
  \item{non.mono.tol}{tolerance for detecting a non-monotonic profile
    and warning/falling back to linear interpolation}
  \item{\dots}{additional parameters to be passed to
    \code{\link{profile.merMod}} or \code{\link{bootMer}}, respectively.}
}
\value{
  a numeric table (\code{\link{matrix}} with column and row names) of
  confidence intervals; the confidence intervals are computed on the
  standard deviation scale.
}
\note{
  The default method \code{"profile"} amounts to \preformatted{
    confint(profile(object, which=parm), signames=oldNames, ...),
            level, zeta)}
  where the \code{\link{profile}} method \code{\link{profile.merMod}}
  does almost all the computations.  Therefore it is typically
  advisable to store the \link[=profile.merMod]{profile(.)} result, say
  in \code{pp}, and then use \code{confint(pp, level=*)} e.g., for
  different levels.
}
\details{
  Depending on the \code{method} specified, \code{confint()} computes
  confidence intervals by
  \describe{
    \item{\code{"profile"}:}{computing a
      likelihood profile and finding the appropriate cutoffs
      based on the likelihood ratio test;}
    \item{\code{"Wald"}:}{approximating
      the confidence intervals (of fixed-effect parameters
      only; all variance-covariance parameters
      CIs will be returned as \code{NA})
      based on the estimated local curvature of the
      likelihood surface;}
    \item{\code{"boot"}:}{performing parametric
      bootstrapping with confidence intervals computed from the
      bootstrap distribution according to \code{boot.type} (see
      \code{\link{bootMer}}, \code{\link[boot]{boot.ci}}).}
  }
}
\examples{
if (interactive() || lme4_testlevel() >= 3) {
fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
fm1W <- confint(fm1, method="Wald")# very fast, but ....
fm1W
(fm2 <- lmer(Reaction ~ Days + (Days || Subject), sleepstudy))
(CI2 <- confint(fm2, maxpts = 8)) # method = "profile"; 8: to be much faster
\dontshow{ stopifnot(all.equal(tolerance = 5e-6, signif(unname(CI2), 7),
               array(c(15.25847, 3.964157, 22.88062, 237.5732,  7.33431,
                       37.78184, 8.768238, 28.78768, 265.2383, 13.60057),
                     dim = c(5L, 2L))))
}
if (lme4_testlevel() >= 3) {
 ## ~20 seconds, MacBook Pro laptop
 system.time(fm1P <- confint(fm1, method="profile", ## default
                             oldNames = FALSE))
 ## ~ 40 seconds
 system.time(fm1B <- confint(fm1, method="boot",
                             .progress="txt", PBargs=list(style=3)))
} else {
    load(system.file("testdata","confint_ex.rda",package="lme4"))
}
fm1P
fm1B
} ## if interactive && testlevel>=3
} 

